Favorite of all time. "Dark Cloud 2"(PS2), i love it, and still play it from time to time. Probably put more hours into that game than any other.
Second, "Mass effect 1/2 and Dragon Age Origins/2"(Xbox360) I love biowares games.
Third would be "Star ocean: Till the end of time/The last hope"(PS2/Xbox360)

I'd have to go with the Super Smash Bros. series. There's just something special about taking your favorite nintendo characters and beating the crap out of them. Otherwise I'd say the Assasin's Creed series.